Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 6 de 6
Filtrar
Mais filtros








Base de dados
Intervalo de ano de publicação
1.
Nucleic Acids Res ; 50(D1): D1273-D1281, 2022 01 07.
Artigo em Inglês | MEDLINE | ID: mdl-34747487

RESUMO

Nanobodies, a subclass of antibodies found in camelids, are versatile molecular binding scaffolds composed of a single polypeptide chain. The small size of nanobodies bestows multiple therapeutic advantages (stability, tumor penetration) with the first therapeutic approval in 2018 cementing the clinical viability of this format. Structured data and sequence information of nanobodies will enable the accelerated clinical development of nanobody-based therapeutics. Though the nanobody sequence and structure data are deposited in the public domain at an accelerating pace, the heterogeneity of sources and lack of standardization hampers reliable harvesting of nanobody information. We address this issue by creating the Integrated Database of Nanobodies for Immunoinformatics (INDI, http://naturalantibody.com/nanobodies). INDI collates nanobodies from all the major public outlets of biological sequences: patents, GenBank, next-generation sequencing repositories, structures and scientific publications. We equip INDI with powerful nanobody-specific sequence and text search facilitating access to >11 million nanobody sequences. INDI should facilitate development of novel nanobody-specific computational protocols helping to deliver on the therapeutic promise of this drug format.


Assuntos
Camelidae/imunologia , Bases de Dados Genéticas , Neoplasias/terapia , Anticorpos de Domínio Único/imunologia , Sequência de Aminoácidos/genética , Animais , Anticorpos/classificação , Anticorpos/imunologia , Camelidae/classificação , Humanos , Imunoterapia/classificação , Neoplasias/imunologia , Anticorpos de Domínio Único/classificação
2.
Sci Rep ; 8(1): 6193, 2018 04 18.
Artigo em Inglês | MEDLINE | ID: mdl-29670147

RESUMO

There are more than 26 million peer-reviewed biomedical research items according to Medline/PubMed. This breadth of information is indicative of the progress in biomedical sciences on one hand, but an overload for scientists performing literature searches on the other. A major portion of scientific literature search is to find statements, numbers and protocols that can be cited to build an evidence-based narrative for a new manuscript. Because science builds on prior knowledge, such information has likely been written out and cited in an older manuscript. Thus, Cited Statements, pieces of text from scientific literature supported by citing other peer-reviewed publications, carry significant amount of condensed information on prior art. Based on this principle, we propose a literature search service, SciRide Finder (finder.sciride.org), which constrains the search corpus to such Cited Statements only. We demonstrate that Cited Statements can carry different information to this found in titles/abstracts and full text, giving access to alternative literature search results than traditional search engines. We further show how presenting search results as a list of Cited Statements allows researchers to easily find information to build an evidence-based narrative for their own manuscripts.


Assuntos
Aplicações da Informática Médica , Sistemas On-Line , Ferramenta de Busca , Pesquisa Biomédica , Humanos , Publicações , Interface Usuário-Computador
3.
Genes Dev ; 31(21): 2175-2185, 2017 11 01.
Artigo em Inglês | MEDLINE | ID: mdl-29196535

RESUMO

Nuclear gene transcription is coordinated with transcript release from the chromatin template and messenger RNA (mRNA) export to the cytoplasm. Here we describe the role of nuclear-localized kinase WNK1 (with no lysine [K] 1) in the mammalian mRNA export pathway even though it was previously established as a critical regulator of ion homeostasis in the cytoplasm. Our data reveal that WNK1 phosphorylates the termination factor PCF11 on its RNA polymerase II (Pol II) C-terminal domain (CTD)-interacting domain (CID). Furthermore, phosphorylation of the PCF11 CID weakens its interaction with Pol II. We predict that WNK1 and the associated phosphorylation of the PCF11 CID act to promote transcript release from chromatin-associated Pol II. This in turn facilitates mRNA export to the cytoplasm.


Assuntos
Transporte Ativo do Núcleo Celular/fisiologia , RNA Mensageiro/metabolismo , Transcrição Gênica , Proteína Quinase 1 Deficiente de Lisina WNK/metabolismo , Fatores de Poliadenilação e Clivagem de mRNA/metabolismo , Núcleo Celular/enzimologia , Núcleo Celular/metabolismo , Cromatina/metabolismo , Citoplasma/metabolismo , Células HeLa , Humanos , Fosforilação , Domínios Proteicos , Interferência de RNA , RNA Polimerase II/química , RNA Polimerase II/metabolismo , RNA Mensageiro/genética , Proteína Quinase 1 Deficiente de Lisina WNK/genética , Fatores de Poliadenilação e Clivagem de mRNA/genética
4.
J Cell Sci ; 129(13): 2514-25, 2016 07 01.
Artigo em Inglês | MEDLINE | ID: mdl-27206860

RESUMO

Centrioles organise centrosomes and cilia, and these organelles have an important role in many cell processes. In flies, the centriole protein Ana1 is required for the assembly of functional centrosomes and cilia. It has recently been shown that Cep135 (also known as Bld10) initially recruits Ana1 to newly formed centrioles, and that Ana1 then recruits Asl (known as Cep152 in mammals) to promote the conversion of these centrioles into centrosomes. Here, we show that ana1 mutants lack detectable centrosomes in vivo, that Ana1 is irreversibly incorporated into centrioles during their assembly and appears to play a more important role in maintaining Asl at centrioles than in initially recruiting Asl to centrioles. Unexpectedly, we also find that Ana1 promotes centriole elongation in a dose-dependent manner: centrioles are shorter when Ana1 dosage is reduced and are longer when Ana1 is overexpressed. This latter function of Ana1 appears to be distinct from its role in centrosome and cilium function, as a GFP-Ana1 fusion lacking the N-terminal 639 amino acids of the protein can support centrosome assembly and cilium function but cannot promote centriole over-elongation when overexpressed.


Assuntos
Centríolos/genética , Proteínas de Drosophila/genética , Glicoproteínas/genética , Animais , Ciclo Celular/genética , Centrossomo/metabolismo , Cílios/genética , Cílios/metabolismo , Proteínas de Drosophila/metabolismo , Drosophila melanogaster/genética , Regulação da Expressão Gênica , Glicoproteínas/metabolismo , Mitose/genética , Proteínas Mutantes/biossíntese , Proteínas Mutantes/genética
5.
Genes Dev ; 27(18): 2025-38, 2013 Sep 15.
Artigo em Inglês | MEDLINE | ID: mdl-24065768

RESUMO

We uncovered a novel role for the spliceosome in regulating mRNA expression levels that involves splicing coupled to RNA decay, which we refer to as spliceosome-mediated decay (SMD). Our transcriptome-wide studies identified numerous transcripts that are not known to have introns but are spliced by the spliceosome at canonical splice sites in Saccharomyces cerevisiae. Products of SMD are primarily degraded by the nuclear RNA surveillance machinery. We demonstrate that SMD can significantly down-regulate mRNA levels; splicing at canonical splice sites in the bromodomain factor 2 (BDF2) transcript reduced transcript levels roughly threefold by generating unstable products that are rapidly degraded by the nuclear surveillance machinery. Regulation of BDF2 mRNA levels by SMD requires Bdf1, a functionally redundant Bdf2 paralog that plays a role in recruiting the spliceosome to the BDF2 mRNA. Interestingly, mutating BDF2 5' splice site and branch point consensus sequences partially suppresses the bdf1Δ temperature-sensitive phenotype, suggesting that maintaining proper levels of Bdf2 via SMD is biologically important. We propose that the spliceosome can also repress protein-coding gene expression by promoting nuclear turnover of spliced RNA products and provide an insight for coordinated regulation of Bdf1 and Bdf2 levels in the cell.


Assuntos
Regulação Fúngica da Expressão Gênica , Estabilidade de RNA , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , Spliceossomos/metabolismo , Mutação , Fenótipo , RNA/genética , Splicing de RNA , Proteínas de Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/metabolismo , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo , Transcriptoma
6.
PLoS One ; 8(6): e65606, 2013.
Artigo em Inglês | MEDLINE | ID: mdl-23755256

RESUMO

A key question in the field of RNA regulation is how some exosome substrates, such as spliceosomal snRNAs and telomerase RNA, evade degradation and are processed into stable, functional RNA molecules. Typical feature of these non-coding RNAs is presence of the Sm complex at the 3'end of the mature RNA molecule. Here, we report that in Saccharomyces cerevisiae presence of intact Sm binding site is required for the exosome-mediated processing of telomerase RNA from a polyadenylated precursor into its mature form and is essential for its function in elongating telomeres. Additionally, we demonstrate that the same pathway is involved in the maturation of snRNAs. Furthermore, the insertion of an Sm binding site into an unstable RNA that is normally completely destroyed by the exosome, leads to its partial stabilization. We also show that telomerase RNA accumulates in Schizosaccharomyces pombe exosome mutants, suggesting a conserved role for the exosome in processing and degradation of telomerase RNA. In summary, our data provide important mechanistic insight into the regulation of exosome dependent RNA processing as well as telomerase RNA biogenesis.


Assuntos
Exossomos/metabolismo , RNA não Traduzido/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo , Saccharomyces cerevisiae/metabolismo , Exossomos/genética , RNA/metabolismo , RNA não Traduzido/genética , Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/genética , Telomerase/metabolismo
SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA